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Shiki is in fact not a real member of the Tohno family, is not Akiha's biological brother, and is not Makihisa's son. While the Tohno family is a family with demon blood, Shiki's real surname is Nanaya, a family of powerful demon-slaying assassins. It is revealed in Kagetsu Tohya that he is the son of Kiri Nanaya. The Nanaya clan lived in a secluded mansion in the mountains, but was one night destroyed by the Tohno and Kouma Kishima. Shiki was the only survivor of that attack. In a moment of amused irony, Makihisa spared and adopted the boy because his name was similar to the name of Makihisa's eldest son, SHIKI (四季, SHIKI?).

Shiki lived in a small Japanese-style building on the grounds of the Tohno's western-style mansion for a time, learning to accept and be accepted by his new siblings. Although he was lonely and unwilling to leave his room at first, eventually he warmed to the cheerful red-haired girl Hisui who would come every day to ask him to play, and in turn lead his shy and often-nervous sister outside as well. He, his sister, his brother, and the red-haired girl would play together frequently.

Eight years before the start of the game, he was involved in a life-threatening accident, which led to anemic symptoms and left him with a large scar on his chest. Due to these symptoms, he suffers from frequent collapsing and fainting. Eight years before the beginning of the game, everything changed. Although Shiki did not know it, the Tohno family's demon blood led to inhuman urges in all its members; every descendant eventually became insane from its effects, a process called "inversion impulse". When this happens, the person loses all ability for conscious thought and becomes a monster with only the mind to kill and consume others. One hot summer day as Shiki played with his brother SHIKI and sister Akiha, SHIKI inverted without warning, and immediately attacked Akiha. Shiki managed to shield Akiha at the cost of his own life; the wound that SHIKI caused by piercing him in the chest became the large scar that Shiki would bear from that day forward.

It is the duty of the Tohno's family head to police demon activity in the area, and specifically to execute any Tohno who underwent inversion so that he or she cannot do the sort of damage that such inhuman beings inevitably do. Makihisa arrived on the scene immediately and, without a second thought, killed his own son. However, neither Shiki nor SHIKI died that day. Although Shiki did not know it then, his sister Akiha provided him with half of her own lifeforce, keeping him alive. In turn, SHIKI instinctively stole half of Shiki's borrowed lifeforce to avoid his own death. It is this lack of energy that causes Shiki's anemic tendencies.

In addition to the physical problems, the accident also caused Shiki's eyes to develop a peculiar ability, the ability to see lines superimposed on objects and people. If Shiki traces these lines with a sharp tool, the object immediately falls apart along them regardless of the amount of force used. Upon discovery of this ability, Shiki understood how destructive it was and how fragile the world around him could be. Because his eyes would not return to normal, the realization began to gnaw at him.

Fortunately, a few days after his time in the hospital, he ran outside and met Aoko Aozaki. Aoko (whom Shiki decided to call Sensei) comforted him during the next few days. Shiki was eager to impress Aoko, thus he demonstrated the ability of his eyes by destroying a tree. Aoko reprimanded him by slapping him and explained to him that what he had done was unjust. Aoko later provided a pair of magical glasses which, when worn, removed the lines from sight.

When Makihisa realized this convoluted state of affairs, he concocted a ruse to deceive the outside world. As the head of a publicly important family, which held an influential position in business, he could not allow others to know that the eldest son of the family had become inhuman, died, or disappeared. To conceal this, Makihisa locked SHIKI away and hypnotized Shiki into believing that he was the Tohno's eldest son instead, erasing the details of that day from the boy's mind. After installing Shiki in SHIKI's place as eldest son, Makihisa then sent Shiki away to live with the Arima family branch under the pretext that a boy so dreadfully injured, and who could die at any time from a fragile constitution could not be the heir to the Tohno house. Despite the necessity of making Shiki believe in his new identity as a Tohno, however, Makihisa retains an antique knife inscribed with the name of the Nanaya clan, and later bequeathes it to Shiki, although the ambivalent nature of Japanese kanji causes Shiki to misread the inscription as "Nanatsu-Yoru", or "Seven Nights".

Because of his poor health, Shiki was removed from the Tohno household by his father, Makihisa Tohno, despite being the eldest son of the family. Instead, he was sent to live with a distant branch of the Tohno family named Arima. He frequented the practice of doctor Sougen Jinan during this time, and once had his first sexual experience with his daughter, Tokie Jinan.[2] At the start of the game, Shiki was called back to the Tohno mansion after eight years of absence due to Makihisa's death, called back by his younger sister, Akiha Tohno. Although he had not seen his sister in those eight years, she has grown into a proper lady of a high-class family, and after removing all of the family residents and servants of the mansion except for a pair of maids, had chosen to invite him to return.

Shiki is a fairly normal high school student most of the time. Due to his close brush with death, he is not overly concerned about dying, and instead seeks to cherish every moment of his life - 'just living is enough' is his perspective on life. He is playful with his sister Akiha and the maids Hisui and Kohaku, sometimes silly, and not at all above exchanging jibes with his best friend and classmate Arihiko Inui or pleasantries with his senior Ciel. He's entirely capable of being serious in a serious situation, and just as often flustered or embarrassed. His personality is one of that who is slightly mean to those he loves. He is also a very, very heavy sleeper, to such a point that Hisui is unable to awaken him.

He has a darker side, that of his bloodline's, the Nanaya. The instincts and skills he had learned at a young age are buried deep within Shiki and have proven capable of manifesting themselves in dire situations, such as in his battle against Nrvnqsr Chaos. Although not on the level of an alternate personality, the Nanaya side of Shiki is the highly trained killer within him and thus is much colder. Only once has his Nanaya side surfaced in a similar way to that of an alternate personality, and that was under great stress and a very difficult situation for Shiki. The other times, Shiki is merely filled with a desire to kill, and instinctual knowledge on how to do it. Sometimes, however, Shiki himself seems to refer to his dark side as "him", another person, namely when discussing with SHIKI. This would imply that he does not fully accept it as his own self. This aspect of his personality seems to have mostly disappeared (or at least rendered obsolete thanks to his mastery of his abilities) after the events of Tsukihime.

Despite the absence of this trait in subsequent stories, however, a remnant of his Nanaya self seems to remain in his usual personality, particularly when he is facing those he considers his enemies. He can be surprisingly cold, giving those such as Nrvnqsr only quick, curt comments while expressing his intent to erase them, or, in the case of Roa, saying nothing at all while exuding a murderous killing intent. However, in each of these scenarios, not once has he ever succumbed to his Nanaya personality, retaining his own sense of self and will, and defeating his opponents on his own terms.

Shiki Nanaya is a manifestation of Shiki Tohno's murderous intent and lives only for his next kill. Nanaya is smooth, confident, and treats life (and death) casually.
Despite his physical condition, Shiki holds a cheerful outlook on life. More so than most of his peers, because he understands how fragile life really is.

While Makihisa began grooming Akiha in earnest as the next family head, Shiki lived with the Arima family branch, which consisted of only a mother, father, and young daughter. The Arima, though related to the Tohno, had negligible demon blood, and he lived there in relative quiet and comfort for eight years.

Despite his family's wealth, Shiki wishes to take up a job because he does not get a monthly allowance from Akiha. She only allows him what food is necessary for him, so extra spending money is unnecessary. She will willingly buy him anything else that he wishes, but he never asks her. They call him unselfish to the point it can be called a medical condition, and he would much work rather than have to ask her.[3]

Shiki first meet Arcueid in one of the 2 "Near side of the moon" routes (Arcueid/Ciel's routes) after leaving school early one day because of an anemia attack, he spots Arcueid on the street and is consumed by an irresistible urge to kill her because of his Nanaya blood. The Nanaya were a family of killers that specialized in hunting down non-humans, and Arcueid as a vampire awoke his Nanaya blood. Skillfully trailing Arcueid back to her apartment, he rings the doorbell and in the instant the door opens, sneaks through the crack and slices her into 17 pieces in an instantaneous single strike with his knife and his Mystic Eyes of Death Perception. Regaining his sanity and finding himself in front of her corpse, Shiki staggers to the park where he either collapses and is taken back to the mansion by Kohaku (Arcueid's route) or is found and taken care of by Ciel (Ciel's route).

The next day when heading to school, Shiki finds Arcueid waiting on a guard rail outside his school. Panicking, he runs, only to be chased into a dead alley and confronted by Arcueid. Their conversation is interrupted by one of Nrvnqsr's beasts, and Arcueid "convinces" Shiki to help her deal with the vampire in the town as she used up most of her power to reform her body after Shiki killed her and will need time to regain the power she had lost.

Arcueid after failing to kill Roa

The two of them are partners against Nrvnqsr Chaos, with Shiki killing Nrvnqsr by striking his "point of death". They decide to again be partners to defeat Michael Roa Valdamjong who Arcueid had been targeting. Over the course of her route she and Shiki begin to understand one another. Shiki shows Arcueid the various things she's unaware of, such as movies, which are things Arcueid can't comprehend as important. Shiki explains that the unimportant and unnecessary parts of life are what make it fun. At several points she attempts to bite Shiki, though she manages to hold herself back in time. Eventually she and Shiki fall in love with one another, despite her slightly unstable nature and vampire lineage. Arcueid, after sleeping with Shiki, attempts to destroy Roa by herself at the school with her Marble Phantasm and is seemingly killed, her weakened body unable to withstand the strain of the skill. Roa, unfortunately, regenerates from the ankles that Arcueid did not destroy, remarking that without the full moon, he would not have been able to recover. Enraged and in grief, Shiki stabs the "point of death" in the walkway he and Roa are on. Roa's body is severely mutilated from the debris and Shiki stabs Roa's point with little resistance. Roa, however, lingers on for a few seconds and attempts to kill the tired Shiki, and is erased from existence by Ciel's Seventh Holy Scripture. Ciel says to Shiki that since she's the one who killed Roa, Shiki should return to the normal world that he came from.

In Arcueid's True Ending, Shiki waits in his classroom for her despite thinking she is dead. Arcueid surprisingly arrives a week after her supposed death, having regained the bit of power Roa stole from her. However, she can no longer hold back her impulses and decides she should sleep from now on, dreaming of Shiki. Despite Shiki's pleas, even begging her to drink his blood, Arcueid says she cannot do so because she loves him and says farewell with Shiki greatly saddened, looking at the moon as he leaves the school. This ending was the basis for the ending used in the anime, although a few details were changed. In the manga, after Arcueid left, he goes on a search for her and they are finally reunited together. It is left unsure whether this is reality or a hypothetical "what-if" situation playing in Arcueid's dream as she sleeps.

In Arcueid's Good Ending, she spends an entire month suppressing her urges and meets Shiki on his way to school, exactly at the same point where he met her at the beginning of the story. The two then go off to seemingly spend the day together.

With the help of Ciel, Shiki successfully defeats Roa. However, he transfers the burden of his madness to him, causing Shiki to have murdering thoughts and strange dreams (one of which Shiki finds about Ciel's past before and after being possessed by Roa). After he gets out of control and gravely injures and rapes Kohaku, Shiki runs away from the mansion, afraid that he will be unable to resist the urge to kill as long as he's around people. Shiki calls Ciel and confesses to her that he's really a killer and needs to be away from people. She asks him to meet her at the school since there are no people there. He goes, but when she shows up she finds her dressed in her executor outfit as she carries her Seventh Holy Scripture. Ciel reveals to him that everything they shared in the past was all a huge lie, and her only purpose for being with him was to find out if he was Roa, and then kill him if he was. Shortly after, Ciel forces them to fight, despite Shiki not wanting to. Ciel quickly immobilizes him, but she is unable to kill him. She tries to convince herself that her love for Shiki was fake and it was just her mission to destroy Roa, but she ultimately collapses, sobbing onto Shiki's arms.

They later go to Ciel's house, when Shiki finds that his body has been excited after Roa transferred to his body. Ciel finds it out and tries a technique on him to calm the soul, in which they have sex. However, after they do it, Shiki is still succumbing to Roa, so he leaves Ciel's house, where he encounters Arcueid, who was looking for him in order to kill him. She immediately blames Ciel for Shiki's current condition and tells him that she can save him if he obeys her. Shiki is given the choice to answer her. If Shiki tells Arcueid that he does not love her, it results in Ciel's True Ending. He attacks her by cutting the line of her neck, causing Arcueid to threaten to kill him for real. Ciel appears and drags Shiki away, before Arcueid recovers. Ciel fights against Arcueid, but she is quickly defeated. Shiki escapes and kills part of the earth in order to sever Arcueid's support from Gaia. Arcueid is slashed on her lines and is forced to retreat to her castle. Shiki, realizing that he is becoming Roa, stabs himself in his point of death. He falls into a dream of his own memories and speaks with his own Nanaya self. After seeing Shiki's determination to wake from his deathly dream, Nanaya dies in Shiki's stead, forever erasing the memories of the Nanaya family from Shiki's mind. Shiki wakes to a sobbing Ciel.

If Shiki tells Arcueid that he is attracted to her, it results in Ciel's Good Ending. After his response, Arcueid kisses him and has him drink a small amount of her blood. This makes Shiki's will stronger than Roa's own. Ciel arrives and says that if Shiki kills Arcueid, Roa will die as well. As both girls prepare to fight to determine how to get rid of Roa, he overtakes Shiki's body, worn out from trying to stop the two. Heeding Arcueid's advice, Shiki slashes the line in his chest in order to kill the weaker "soul" within himself. After that, he has a vision of Roa before he started reincarnating and Roa dies. After killing Roa, both Ciel and Arcueid "share" Shiki, resulting in a sort of harem ending much to Ciel's chagrin.

Shiki returns to the Tohno house after years. He fondly remembers the times he spent with his sister Akiha. He also feels guilty because of the strict upbringing she received after he had to left the Tohno house. Unfortunately for Shiki, his reunion with Akiha is not exactly as he had hoped it to be. She is cold and distant to him, immediately demanding that he adopt a lifestyle befitting of the eldest son of the Tohno family. Akiha scolds Shiki over everything, which causes him to believe that she might bear a significant grudge over his absence the last eight years. When Shiki goes to school, he realizes that his classmate Satsuki is gone. Later it is revealed that she was turned into a vampire by SHIKI.

When Shiki, who had just crossed ways with Satsuki, returns home he is scolded by Akiha but she later treats his wounds. The next day, Shiki decides to confront the vampire Satsuki after he promises to Akiha that he would come back home safe. Satsuki tries to turn him into a vampire to be with her forever, and at that moment Shiki realizes his feelings for Akiha and their promise. Motivated by it, he kills Satsuki, although regretfully. When he returns home, he notices that Akiha was waiting for him the whole time and she chastises him for returning wounded.

Akiha decides to spend more time with Shiki by joining into the same school at him. Like Arcueid, she does not like Ciel. It is revealed through the route that Akiha often struggles to maintain control over her Tohno blood and resisting her Inversion Impulse, which she has difficulty with due to her also maintaining Shiki's life, to the point she also had to drink Kohaku’s blood. When Ciel vanishes, Akiha reveals to Shiki that she always knew that Ciel was different and she was unaffected by her hypnosis. Due to the recent killings in the city recently, Shiki believes that Akiha might be the vampire who did it and goes to the Tohno house. When he arrives, he sees Akiha unconscious and that SHIKI is there. He tells him that he went to take Akiha "back with him" and reveals to Shiki all the truths of their childhood. However, Akiha regains consciousness and protects Shiki. The two have a confrontation about Shiki, only for Akiha to say in his face that Shiki is her brother now and that she does not consider SHIKI as her brother anymore. SHIKI is angered of this revelation and aims to kill him, but Akiha protects Shiki and takes the attack. This causes Shiki to have a homicidal impulse and cut SHIKI’s lines. After that, Akiha and Shiki talk in her room, where she tells him that in fact, Shiki was adopted after SHIKI killed him and due to it, their minds are connected and he took a part of his life (she also tells him that she believes that one of the causes of their connection might be related to the fact Shiki and SHIKI used to be best friends when younger). Then, she starts having spasms and her hair turns red. Akiha confesses to Shiki that she was aware from the beginning that he is not her real brother, but she felt that it was the only way for her to be with him. However, Shiki reassures her that he loves her as a sister and a woman and they kiss and have sex together. After this, SHIKI is filled with jealousy and reveals to Shiki that Akiha has been maintaining his life since he died eight years ago. Akiha is later kidnapped by SHIKI. Later, when Shiki comes to the abandoned room in order to confront SHIKI and save Akiha, he discovers that SHIKI turned her into a mindless, bloodsucking creature and apparently he raped her offscreen. Both fight and Shiki manages to debilitate him. However, at the last moment, Shiki hesitates to kill him so SHIKI uses the last of his energy to return to the abandoned house and see Akiha. Surprisingly, Akiha, now a mindless monster, kills SHIKI by ripping his heart out. Shiki is given three choices:

-To kill her to end her suffering (which she requested for him to do if she ever became like this). This gives no special ending and is considered a bad end.

- To allow her to live on as the demon that she currently is (because Shiki cannot bring himself to kill her). This results in Akiha's Normal Ending, where Shiki maintains Akiha at the abandoned room and tries to contain her bloodlust by himself, by routinely letting her painfully bite him and suck his blood out of the wound, all the while hoping that someday she will find herself again.

- To kill himself (so that she will regain the life energy she gave Shiki when he died eight years ago, and then will be restored to her full strength so she can more easily resist her Tohno blood impulses and restore her mind). With this, Akiha's True Ending is obtained, in which Akiha regains her sanity and when she wakes up, she realizes what Shiki did. Akiha is able to live a normal life and returns to her old school. One day, she goes to the place where he died and sees Shiki's Nanatsu Yoru knife. Despite the fact that Shiki should be dead, Akiha touches the knife and senses deep inside her that there still seems to be a faint heartbeat that is not her own. She recognizes this as a sign that Shiki is still somehow alive somewhere, and that as long as she feels it, she has hope, and declares that she will faithfully await his return.

In Kagetsu Tohya, a 'sequel' scenario to Akiha's True Ending can be unlocked where at the end of the scenario, Akiha receives a letter from Ciel that reveals that Shiki did in fact survive.

Shiki returns to the Tohno house after 8 years. He remembers about a cheerful girl he got along with and a quiet girl who gave him a ribbon, but he cannot remember their names. After meeting with Hisui and Kohaku, Shiki mixes the two maids up, believing Kohaku to have been the girl he always played with and Hisui the girl who stayed in the mansion. Hisui's demeanor has changed so much, that rather than being the active girl he knew as a child, she has become severe and emotionless. During the Welcome Party for Shiki, Hisui, not used to drinking but wanting to do it for Shiki, drinks only one glass and then falls asleep. Shiki carries her to his room so she could rest and then he falls asleep as he remembers that the first person he met at the Tohno house when he was a kid was a cheerful girl who convinced him to play outside with the others. When he wakes up, he finds that Hisui is sleeping on top of him, but apparently nothing happened.

Hisui, because she knows of the abuse inflicted upon Kohaku, refuses to let any male so much as touch her, the one exception being Shiki later in her path. Still believing Hisui to be the quiet girl who gave him the ribbon, Shiki gives Hisui the ribbon back.

More and more about her personality and who she truly is revealed. Rather than the stern, immovable young lady she appears to be, Hisui is revealed to be a kind, loving and emotional girl, hiding her emotions to keep her sister as she is. Becoming a daily part of Shiki's life, Hisui wakes him up every day and prepares his uniform. However, she is hiding a darker secret, as she knows of her sister's plans for the downfall of the Tohno family, and after Shiki becomes paralyzed due to SHIKI stealing his life energy, Hisui offers her ability to Synchronize with Shiki so that he can stop SHIKI. She then accompanies Shiki as he goes to the school.

In Hisui's True Ending, after Kohaku reveals that she was responsible for the deaths of Akiha and SHIKI, she commits suicide by stabbing herself in the chest to end her "doll's existence". However she has no regrets, since due to her sacrifice Hisui was never touched by Makihisa. Hisui begins a relationship with Shiki and later accompanies him on his vacations. Before going, she throws Kohaku's ribbon to the sky, "returning" it to its rightful owner.

In Hisui's Good Ending, after Kohaku reveals the truth about her participation in the downfall of the Tohno family, and claims that she hated Shiki because, unlike the others, he always acted like he wanted her to come outside to play with him. Hisui appears and tells Kohaku that what she is saying is not true and that she truly loved Akiha and Shiki. She also tells her that if Kohaku was genuinely attempting to take on her role, using Hisui's original cheerful personality as her own, to never hate Shiki is an integral part of it. After Hisui's words, Kohaku ingests poison in order to commit suicide. She is saved by Shiki, who cuts the "lines" of the poison within her. She later loses her memory and she is renamed "Nanaya" by Shiki and Hisui, and returns as a peaceful maid to the Tohno Mansion. After that, Hisui takes Shiki to her favorite spot to see the city together.

Shiki returns to the Tohno house, where he is greeted by Kohaku. Like in Hisui's route, he wants to give back the ribbon that the quiet girl who watched him from afar when they were young, gave him; but he mistakes that girl for Hisui. During the Welcome Party for Shiki, after drinking all night, Shiki goes out to cool a little where he talks with Kohaku about the quiet girl, the ribbon and the promise. Kohaku looks at him with concern as she warns Shiki that he will only find suffering in the Tohno house and wonders aloud why did he have to return. Noticing that Shiki is intrigued about the mysteries about his past, Akiha tracks down and kills SHIKI before Shiki even starts having dream visions of him. Kohaku helps her in doing so.

Hisui reveals to Shiki that Kohaku is the girl who gave him the ribbon in their past. Due to SHIKI's ability of immortality and the nature of Akiha's powers, he transfers the burden of his madness caused by the inversion impulse of his Tohno blood over to her when Akiha absorbs his energy to kill him. After this, Akiha begins to slowly succumb to the Tohno blood, despite her originally being quite capable of controlling it. She synchronizes with Kohaku in an attempt to suppress this, but it is not enough, since she now has SHIKI's bloodlust itself. She begins hunting for victims on the streets at night in SHIKI's place because she can't control herself, with only Kohaku being aware of it.
Kohaku reveals everything to Shiki and comments that Akiha is out of control. According to her, the only way to stop it is by reciprocating Akiha's feelings for Shiki. However, Shiki refuses to do such thing because he loves Kohaku and returns the ribbon to her. He says to Kohaku that he knew she was the girl in the window because their promise was made not outside the gates of the mansion as Hisui said, but at the tree in the garden. Kohaku cries and decides not to continue with her revenge on the Tohno family. She and Shiki have sex and she offers her ability to Synchronize with Shiki so that he can stop Akiha. However, Kohaku then tricks him into swallowing a sedative so she could go by herself, atoning for her actions. Shiki is able to resist and goes to the school. There, Akiha tells Shiki that the Tohno family has wronged Kohaku to an incredibly degree and everyone, even him, to Kohaku, are just pawns to her revenge. However, Shiki tells Akiha that he loves Kohaku no matter what, prompting her to attack Kohaku by piercing her chest with her hair. Shiki is devastated by this and attacks Akiha, however he realizes that he cannot bring himself to kill her. At that moment, Kohaku appears, seemingly with no fatal wounds, telling Akiha to stop because she holds no resentment towards her and she has already forgiven the Tohno family. Akiha realizes that the reason why she did not succeed in killing Kohaku is because she subconsciously did not want to kill her.

Kohaku is the only character with only one ending, which is also her True Ending, in which she decides to forgive the Tohno family and goes on a vacation with Shiki to the Nanaya forest.

Shiki rests and relax in a grass field and meets with Aoko Aozaki once again at night. After he tells his teacher about what he experienced, Shiki is told that he has not much longer to live. Aoko feels guilty that Shiki tried so hard to live a moral life as according to her suggestion, when he would have had a much easier time had he "broken" completely. Shiki replies that even so, he was happy living such a life and that Aoko has nothing to feel sorry for. After Aoko tells Shiki that he had truly grown up to be a wonderful man, the two part ways, never to meet again.

One year after events of Tsukihime, while rushing to school, Shiki sees a truck about to hit a cat, and saves it. He is able to dodge the truck, but hits his head on the sidewalk, being sent to the hospital shortly afterwards.

He enters into a dream world where the same day would repeat over and over, thanks to Len.

Shiki does not realize that he is dreaming so he continues living his life normally. Unaware of anything around him until the world crumbles due to Len's mana running out, he starts to notice strange things that happen around this world such as a hallucination of the world's end, a mysterious killer, his encounters with Len in both human form and cat form and a vague memory from the previous day.

Shiki tries to solve the murders and fights the killer, who is revealed to be Shiki Nanaya. He wins instantly in the first night, but after the same day repeats, Nanaya appears before him again and meets with him several times outside the mansion and his school.

Eventually, Shiki faces off with Nanaya once again. Nanaya complains about their last fight, though Shiki does not remember it. They fight but Shiki is overwhelmed and killed after noting that Nanaya had mastered the Nanaya Arts that he would have learned if his clan was not destroyed.

At night, Shiki sees through Nanaya's eyes in his nightmare. He learns that Nanaya chose Len as his next target, realizing that she is the reason that he could not permanently kill Shiki. When he awakens, Shiki desperately makes his move and confronts Nanaya before he can achieve his goal. It is revealed that Nanaya is a nightmare manifestation version of Shiki himself, embodying his greatest fear. Unlike before, Nanaya lets out his urge by repeatedly throwing his knife at Tohno instead of fighting him using his technique or instinct. After their short fight, Kouma Kishima, an incarnation of the "death" of the world itself, appears and crushes Nanaya. After this death, Nanaya does not appear in the dream.

Len kisses Shiki.

As long as Kouma exists, Shiki cannot go back to his world because of Len's state. Len decides to settle things, giving him a farewell kiss and going off to face Kouma alone. In next day, Shiki goes to a place from his childhood, Nanaya's Forest. Just as he thought, he meets with Kouma and the nearly dead Len. He claims that he could endure Kouma's attack 3 times, but is surprised that he can endure far more. After realizing that the concept of "death" that Kouma embodied was weakening every time Shiki blocked or dodged his attacks, Shiki calls Kouma a fake and uses his Mystic Eyes of Death Perception to kill Kouma.

After everything is settled, he meets Len at a tea garden and forms a contract with her, leaving the dream world.

The story seems to take place after the "Normal Ending" of Satsuki Yumizuka's route in Tsukihime (which was never implanted in the Visual novel). The route followed the same events as Arcueid's route but the situation of each heroine didn't change. In the Manga it is mentionned that Shiki had to kill Satsuki, not being able to save her like he had promised. The story is extended when Wallachia manifests as Satsuki and Shiki has to face her and kill her an another time. In the scenario of MELTY BLOOD ReAct, Shiki never killed her.

After hearing rumors about a vampire killer, Shiki decides to patrol around the city to figure out what was happening. During one of his patrols, he meets for the first time Sion Eltnam Atlasia. Later on they meet each other again at night time and she assaults him. Whether he looses against her or not, he joins her in order to help her find the cure to her vampire impulses. In a certain route of the game (or the one portrayed in the Manga), the Night of Wallachia will manifest as Nrvnqsr Chaos and Arcueid and make Sion succumb to her vampire side. After overcoming all these obstacles, Shiki and Sion won't be able to kill TATARI because he doesn't have a body. The true Arcueid will eventually show up and create a scenario where the Crimson Moon makes an appearance, forcing Zepia Eltnam Oberon to manifest in his Dead Apostle form. This situation then allowed Shiki and Sion to ultimately kill him.

Wandering around the city, he meets an another time with Sion but seems to not recognize her. She tells him to not involve himself in the current events and attacks him like in Melty Blood. After beating Sion, he asks Kohaku to take care of her, saying that he would apologize himself to Sion after dealing with everything that was happening.

Facing many adversaries, Shiki goes to the park in order to respect his promise he made to Arcueid but he is welcomed by Red Arcueid. Shiki notices that she isn't the real Arcueid making her reply the fact that she doesn't want to people to confond her with the real one, declaring that she is the manifestation of her vampire impulses. She explains that she took form because of the Reality Marble that was around the city and that she would disappear at dawn. Before that, she says that she want him the be hers, specially his eyes, attacking him directly.

After this fight, Shiki starts remembering about the Night of Wallachia. Going to the Sanctuary, he meets Riesbyfe Stridberg who was garding the entry. She orders him to leave because humans with talents like his weren't allowed to stay in a place like this. However Shiki says to her that he would never have reached this place without it and tells her that compared to the other people he met in his way, she is the first one that he didn't know the face. She states that she wasn't waiting any less from the one that defeated the Night of Wallachia and that he was able to destroy the Reality Marble they were in without any kind of magic, engaging a fight with him.

Passing Riesbyfe, Shiki is finally able to see the Dust of Osiris and shows himself dazed in front of all the jewels that were in their surroundings. She explains that the jewels are Philosopher Stones, also called "Aqua Vitae" or "Water of Life", that allowed her to use TATARI. Shiki notices then that she is in fact Sion et remembers that he already had defeated TATARI and stays surprised over the fact that it came back. The Dust of Osiris also shows herself surprised over the fact that he recognized her as Sion, tells him that he is the greatest anomaly here. As Shiki tries to ask her how did she finished like that, notices that the stone are made of lines of death.

She explains that she wanted to reproduce the Night of Wallachia in order to change the ending where he kills Zepia because according to her, he is the reason why her other self exists and the reason why she will cease to exist. If he disappears, she will be able to become the only Sion. It is revealed that she is a Sion created by TATARI to kill Shiki in order to make the world where they were, real.

Shiki will defeat her eventually putting an end to TATARI. He then meets again with the Sion of his world, who tells him that this was the best ending that the Dust of Osiris could have, because for her, being destroyed by Shiki Tohno, is a salvation. She asks him to never forget the feeling he got when he was around her. This request makes him reply that he couldn't forget about her that easily because he was allowed to see how Sion would like when she would turn adult. Sion instantly takes it as a perverted remark and, embarrassed, she takes out her gun, telling him to forget about that.

Shiki appears in Talk. and Prelude under the name DEATH, one year after the events of Tsukihime.[4]He is referred to by Merem Solomon as Shiki the Killer (殺人貴, Satsujinki?), wordplay on Shiki's name (志貴?) and Killer Demon (殺人鬼, Satsujinki?) that was first used as a joke in a Teach me, Ms. Ciel ending. Satsujinki is commonly confused with DEATH as the pseudonym he was operating under at the time, but in fact, only Merem called him that. He had gradually become a rumor after gaining much fame, still the "same fool with a knife-fetish" accompanying Arcueid while complaining ceaselessly.[5] He is a shadow like a Death God, deemed an elusive calamity in the world of Dead Apostles like Enhance.[6] He wears bandages over his eyes rather than his Mystic Eye Killers, and he must unwind and wind them before and after battles. as they lost their effectiveness after constant usage of his eyes. Because of this, he must unwind and wind the banages before and after battles. He still wields his knife, and wears simple attire that is lacking in resistance compared to someone who would normally fight. Although both stories were written as introductions to a possible Tsukihime 2, there have been no further developments with the storyline.

During Talk., Shiki travels to Germany on the tip of a third party rather than a whim of Arcueid in order to seek out the Fruit of Einnashe for the benefit of reducing her bloodlust. He encounters Forte, and he easily defeats her despite placing no wounds upon her. She considers it her complete defeat, and asks for his name, though she is unable to understand his reply in Japanese. He then encounters Merem Solomon projecting his voice from outside his body, who notes that while they were to eventually meet, he had not thought it would be that soon. He describes Shiki's motivations in coming being similar to Ciel.

Shiki has a hard time understanding his English because he cannot speak it fluently, reacting to the mention of Ciel's name. Shiki displays a brief moment of killing intent, but Merem manages to calm him, saying that Shiki could not kill him because his body was actually elsewhere. Merem calls him honest in doing so, and though he had thought Shiki would be an emotionless killer, he instead describes Shiki as a contradiction whose purpose divides into two extremes, more specifically two completely different systems of thought. Merem guides him Einnashe's heart in exchange for an explanation of Einnashe's nature Shiki heard from Arcueid.

Merem relays the story to Ciel, and she deduces that it must have come from someone close to her. Merem confirms Shiki is within the forest in order to kill it, and notes that Shiki also muttered something about being amazed that she was there as well and flushed red from embarrassment. The forest begins to quake as it senses something capable of killing it approaching, and he manages to successfully kill it. He encounters Ciel, and she does not pursue him even though the Church had ordered for his capture as an important reference.

Prelude features him going after Louvre in order to steal a notably strong mace from his collection of magical wares. He manages to sneak into Louvre's castle while his minions, Barthomeloi Lorelei and her subordinates, and Enhance are battling, reaching his lair by cutting a hole in the ceiling as Louvre and his two children prepare to face the known threats. Though their power together should be at its height, he easily kills all three before they are able to notice him, takes the mace, and leaves before the others arrive. Lorelei, her pride severely damaged by having her prey taken from her, promises revenge upon Shiki for his actions.

In terms of potential, Shiki even surpasses his father Kiri Nanaya, the most powerful assassin in the history of the Nanaya family.[7]

Shiki's primary weapon is a small knife, a relic of the Nanaya family named Nanatsu-Yoru (七夜, Nanaya?, Seven Nights). It is a switchblade with a plain hilt, with its blade and hilt of a length around 10 cm. The blade can alternately be called the Nanaya, taking after Shiki's real surname. The meaning of the name is the same as well as the kanji.

Because of his Nanaya training as a child, Shiki possesses excellent physical ability, capable of feats comparable to at least an Olympic-level athlete. He is capable of two unique styles developed by the Nanaya: Flashing Scabbard (閃鞘, Sensa?), the ability to attack extraordinarily quickly, with an example being his Seventeen Divisions move spawned from Flashing Scabbard: Monk Imprisoned by Doubts (迷獄沙門?), and Flashing Dash (閃走, Sensō?), the ability to essentially "teleport", or move so quickly that one loses sight of him in an instant. These types of attacks are also shown to be styles branched into other attacks from the clan such as Flashing Scabbard: Eight Point (八点衝?) or Flashing Dash: Six Hares (六兎?), which Shiki's Nanaya persona usually shows focus on. Shiki is primarily an instinctual fighter, relying on his subconscious knowledge of assassination techniques; however, he has only learned the basics of the Nanaya Arts as a child, due to Kiri Nanaya abolishing the demon hunting practice. He possesses the Nanaya family's characteristic murderous impulse against non-humans, but this appears to be, in most cases, a controllable impulse that is mainly meant to enhance his Nanaya Arts. It is suggested in the Near Side Routes, specifically in the battle against Nrvnqsr, that he possesses detailed knowledge on the human anatomy.

His endurance has a ceiling due to his limitations as a human, and his battle style usually involves guarding and dodging until the chance for a decisive attack presents itself.[8] When he is in dangerously close proximity to death, his Nanaya persona resurfaces and he regains the basic Nanaya Arts that he lost from Makihisa Tohno's hypnosis. As Shiki Nanaya, he becomes an assassin who is focused completely on eliminating his target. In this state, it seems that he is even more difficult to kill than usual; however, this is merely a facade. All he does is ignore any sense of pain or threat to his life in order to kill his target through sheer force of will; this creates the illusion that he is somehow capable of delaying his death for as long as he needs to.

Shiki's fighting abilities are enhanced in Melty Blood due to having to fit with the story and allow him to act as a protagonist that can "fight normally," and he appears to be able to use the basics of the Nanaya Arts that he learned as a child without limitations. Shiki, who can participate in combat only by means of trump cards, a "3 of Hearts" in Tsukihime, can fight normally as a "Jack of Spades" in Melty Blood.[9]

Shiki's signature ability may be his ability to see the "death" of things: the Mystic Eyes of Death Perception. After coming into contact with death twice, with the extermination of the Nanaya and his death by SHIKI, his brain became able to comprehend the concept of "death" and this modified his Pure Eyes into eyes connected to the Root itself. With these Mystic Eyes, Shiki is able to see the eventual fated destruction of an object or entity expressed as small points on the object or entity's body and as thin black lines that extend from those points and crawl over the body. Tracing the lines does not require much exertion; doing so effectively realizes the fated destruction of the part that has the line, and the victim is cut along those lines. Because this destruction is destined, this method of injury ignores any of the victim's defenses; armor, magical protection, regeneration, and so forth are useless. While a line symbolizes the death of only a part of an existence a point symbolizes the death of the existence itself. When a point is pierced, the victim's "concept" is destroyed. This method of killing is apparently absolute; it bypasses even reincarnation, and can even be used against a collective entity. The only entity he has failed to kill is Night of Wallachia, since it does not exist as an actual being, but instead as a phenomenon that does not "exist" until it occurs. Nasu has also stated that beings such as ORT are immune to Shiki's Eyes, having no concept of "death" in the first place due to being an extraterrestrial Ultimate One.

The Mystic Eyes of Death Perception are not infallible. The human mind was not meant to perceive death in such a way, and using it is highly taxing on the human brain, causing painful headaches. This is partially the cause of Shiki's frail condition and his frequent anemia. In addition, there are multiple levels of perception; in the beginning, Shiki could only see lines on people and objects, then progressed to seeing points on living things, then points on inanimate objects. Each step takes the mind further from natural perception, and each step is more damaging to the brain; eventually the stress leads the brain's blood vessels to burst and death for the user. In addition, there exist in nature entities which have no fated destruction in particular circumstances such as Arcueid during the night when she is at her strongest. In these cases, no lines or points can be seen. Lastly, the ability to perceive and trace lines or pierce points does not give the user any added physical capacity to perform the task itself. Shiki must still get in range, aim, and strike the target himself, which is not a trivial task against the kind of enemies he faces.

Shiki Tohno [Person's name]
The protagonist of Tsukihime. Afflicted with chronic anemia. Mister Glasses.
He is the kind of character that makes both friends and enemies without realizing it. His habit of collecting edged weapons is probably a trait left over from the "other" Shiki, from Kara no Kyoukai. Taking his glasses off for every single event CG is his charm point.
An unfortunate boy, who suffered through various ordeals in Tsukihime, was dragged into strange situations in Kagetsu Tohya, and had a terrible time in Melty Blood.
Because he lived true to his promise with Aozaki Aoko to "become a man in the manner he thinks is right", he developed into a good and upright person, but at his core he is actually comparatively cold-hearted. Or rather, no matter what happens, good or bad, he simply accepts it as it is. In a sense, this reckless way of life is similar to that of a hermit who has retired from society.

Shiki the Killer [Colloquial Term]
The person Merem called Shiki the Killer. Needless to say, it was that person.
One year after the story of Tsukihime, he gradually became a rumour. Such was the fame of this person.
He was still the same fool with a knife-fetish.
By the way, he still kept the whimsical Princess company while ceaselessly complained. It seemed he came all the way to Germany not because of the whim of the Princess, but due to the tip of some third party.

Death [???]
Assassin. One who could slice the unbreakable like butter, and dismember the indestructible Dead Apostles. As the name suggested, a shadow who was like a Death God.
Like the Avenger, he was deemed an elusive calamity in the world of Dead Apostles.
.... running around doing errands with no pay, what a hard working guy.

↑For that reason, frantically guarding against the absurd attacks of absurd opponents is his fighting style. His defense is weak and you'll see him KOed often just with pokes; however, if he is able to get in close, that's when he shows his worth as a main character!...Once he attacks, death is unavoidable. - Type Moon 4th Character Popularity Poll

Since this was a fighting game, the position of the protagonist, Tohno Shiki, a character that could participate in combat only by means of trump cards, was reversed, and he became involved in the story as a protagonist that can "fight normally".

"....Right. The characteristics of the characters in "MELTY BLOOD" had either been exaggerated or restrained from what they had been in Tsukihime."
"Using cards as an example, Shiki of Tsukihime would be a 3 of Hearts. But the Shiki of "MELTY BLOOD" would be able to fight normally as a Jack of Spades."